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Molecules 2010, 15, 5079-5092; doi:10.3390/molecules15085079 OPEN ACCESS molecules ISSN 1420-3049 www.mdpi.com/journal/molecules Article Functionality Pattern Matching as an Efficient Complementary Structure/Reaction Search Tool: an Open-Source Approach Norbert Haider Department of Drug and Natural Product Synthesis, University of Vienna, Althanstraße 14, A-1090 Vienna, Austria; E-Mail: [email protected]; Tel.: +43-1-4277-55624; Fax: +43-1-4277-9556. Received: 9 July 2010; in revised form: 22 July 2010 / Accepted: 26 July 2010 / Published: 27 July 2010 Abstract: An open-source software package for creating and operating web-based structure and/or reaction databases is presented. Besides standard search capabilities (text, structure/substructure/similarity), the system offers a fast additional search option, entirely based on binary pattern matching, which uses automatically assigned functional group descriptors. Keywords: open-source; checkmol; matchmol; functional groups; structure databases 1. Introduction The management of compound archives usually requires a carefully designed and well-maintained compound database system. Web-based solutions are very attractive for such a purpose, as they can offer all or parts of the available information to a broader public without requiring the installation of dedicated software on the client side. The NIH/NCBI PubChem database may serve as a typical example of such a web-accessible chemical compound database with full support of structure/substructure search [1]. This very large collection of structures and associated data currently contains more than 40 million entries; and whose cheminformatics infrastructure was built around OpenEye’s OEChem library [2] and the Cactvs toolkit [3,4]. Various other software products suitable for running a web-based chemical structure database are available, such as the JChem package from ChemAxon [5], but most of these solutions are commercial products and thus closed-source applications. Among the open-source projects, the Chemistry Development Kit (CDK) [6] deserves particular attention, as it provides a powerful and flexible framework of Java routines which can be Molecules 2010, 15 5080 integrated into various kinds of cheminformatics applications, including web services. Other promising open-source approaches aim at the extension of general-purpose database management systems like MySQL [7], PostgreSQL [8], or Oracle [9] with add-on modules providing structure/substructure search functionality and other features of ―chemical intelligence‖ by extending the syntax of the Structured Query Language (SQL), e.g., via integration of the Open Babel chemistry toolbox [10]. An overview of these projects like Pgchem [11] can be found at the ChemiSQL Wiki website [12]. By nature, all of these toolkits/frameworks/add-ons require some amount of programming in order to assemble them into a fully functional website with structure search capabilities. While this software integration effort is easily feasible in institutions with sufficient cheminformatics expertise and/or software development/support personnel, it may pose a problem for smaller units (e.g., experimentally oriented chemistry research groups) wishing to share their small to medium-sized collections of chemical structures via a website. With this need in mind, a software package was developed and made freely available which is easy to install and manage, but offers all of the essential search options. In the following, the principal features of the current release of this package, MolDB5R [13], will be described and its special capabilities for handling information about functional groups in molecules will be discussed in more detail. 2. System Description 2.1. General Concept The MolDB chemical database software was developed as a compact application package which runs on top of a combination of very common hard- and software. As hardware, any industry-standard x86 PC can be used and Linux was chosen as the primary operating system (MS Windows is also supported with some limitations). Web server functionality is provided by the popular Apache software [14] in combination with the PHP scripting language [15]. For storage of chemical structures (as molfiles) and associated textual and numeric data, the MySQL relational database management system [7] is used. All of these components are open-source software and they are included in most Linux distributions. The MolDB5R package (see Figure 1) consists of a set of PHP scripts which provide the user interface for the various search options. The central element for chemical structure/ functionality analysis and structure comparison is provided by the open-source program, checkmol/ matchmol [16] which will be described in more detail below. For setup and administration of the system, a collection of utility programs written in the Perl scripting language is included. For instance, there are scripts for batch import and export of compound data in the commonly used MDL SD (structure+data) or RD (reaction+data) file formats [17]. As a tool for input and (to some extent) display of chemical structures on the web pages, the JME Java applet is used, which is freely available from its author, P. Ertl [18,19]. The main features of the MolDB5R package are: text search in structure and reaction data collections structure/substructure/similarity search in structure data collections structure/substructure search in reaction data collections functional group search in structure and reaction data collections administration front-end for entering/editing structures or reactions and associated data Molecules 2010, 15 5081 For structure/substructure search operations, a typical two-stage process of efficient pre-selection and subsequent atom-by-atom comparison (subgraph isomorphism) of the query structure with the candidate structures is used. The checkmol program is employed for the generation of pre-selection descriptors (fingerprints) whenever a new structure or reaction is entered into the database, while its companion program, matchmol, is responsible for the final structure-matching operation. Figure 1. Client/server architecture of MolDB5R. Web browser JME applet Client Query Hit structures Internet / structure + data Intranet Query + candidate structures checkmol/ PHP scripts matchmol or Web server Query fingerprints cmmmsrv Hit identifiers Server SQL Candidate structures + data Relational database (MySQL) 2.2. Analysis of Chemical Structure and Functionality with Checkmol With its origin in an educational software project, the checkmol program has grown into a multi- purpose tool which offers a variety of analysis functions. It is a compact command-line program written in the Pascal language. It reads chemical structures in MDL molfile format [17] either from a disk file or from standard input, the results are always written to standard output (i.e., to the screen in a text-based console). Depending on command-line options specified, output can be as follows: a list of all detected functional groups in clear text (English or German) the same list as a bitstring (in 32-bit segments, each represented as unsigned integer number) the same bitstring in ASCII representation (i.e., as a string composed of ―0‖ and ―1‖ symbols); in both representations, each position in the bitstring represents the presence or absence of a particular functional group in the molecule a list (in one of two possible output formats) of discrete structural descriptors (―molecular statistics‖ = ―molstat‖), useful for pre-selection in a structure database a list (in one of two possible output formats) of hash-based fingerprints, useful for pre- selection in a structure database the chemical structure in MDL molfile format with additional encoding for aromaticity Molecules 2010, 15 5082 Whereas some parts of the program are always involved, such as ring search and aromaticity detection, other subroutines are only invoked on demand, depending on the command-line options which have been specified (see above; some of these options can be combined). A typical workflow is depicted in Figure 2. Figure 2. Main workflow for analysis of a chemical strucure by the checkmol program. molstat analysis structure ring aromaticity functional output input search detection groups fingerprint generation In order to reliably detect all aromatic structures, a ring search is performed, using the set of all rings (SAR) [20] as the default ring set (with a fallback option to a smaller ring set for highly con- densed systems). These rings are then examined for their aromatic character, applying the following criteria: the Hückel rule of 4n 2 electrons must be met and conjugation must not be interrupted. Charged atoms (like in the cyclopentadienyl anion or in the tropylium cation) and heteroatoms with free electron pairs (like in furan) are considered as well as mesomeric structures contributing to aromaticity (like in 2- or 4-pyridones). As these detection routines require some computational effort, it appears reasonable to perform them only once during entry of a new structure into a database and to store this information permanently in a suitable manner. For this purpose, checkmol can generate a slightly modified (―tweaked‖) molfile output in which aromaticity information for atoms and bonds is contained transparently in unused columns of the tabular molfile data structure. After completion of aromaticity detection, all atoms of a molecule are classified into subtypes (in addition to elemnt, iso- tope,
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